A Finite Element Method (FEM) is presented to determine reflection and transmission coefficients of rectangular waveguide junction discontinuities. An H-plane discontinuity, an E-plane ridge discontinuity, and a step discontinuity in a concentric rectangular waveguide junction are analyzed using the FEM procedure. Also, reflection and transmission coefficients due to presence of a gap between two sections of a rectangular waveguide are determined using the FEM. The numerical results obtained by the present method are in excellent agreement with the earlier published results. The numerical results obtained by the FEM are compared with the numerical results obtained using the Mode Matching Method (MMM) and also with the measured data.